chr19-33299596-A-G

Variant names:

• chr19-33299596-A-G
• rs10403561

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.464 in 151,938 control chromosomes in the GnomAD database, including 16,851 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (16851 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.404
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.576 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70359 AN: 151820 Hom.: 16809 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.464

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.464 AC: 70445 AN: 151938 Hom.: 16851 Cov.: 32 AF XY: 0.460 AC XY: 34124 AN XY: 74262

African (AFR) AF: 0.582 AC: 24120 AN: 41418

American (AMR) AF: 0.393 AC: 5999 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1413 AN: 3468

East Asian (EAS) AF: 0.461 AC: 2365 AN: 5132

South Asian (SAS) AF: 0.428 AC: 2060 AN: 4818

European-Finnish (FIN) AF: 0.372 AC: 3936 AN: 10578

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28953 AN: 67938

Other (OTH) AF: 0.459 AC: 966 AN: 2106

Alfa AF: 0.440 Hom.: 13008

Bravo AF: 0.471

Asia WGS AF: 0.434 AC: 1513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.66
PhyloP100		0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10403561; hg19: chr19-33790502;